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Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3 bound to pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.8 M Sodium phosphate monobasic monohydrate, 0.8 M Potassium phosphate monobasic, 0.1 M HEPES sodium pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.4 63.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.172 α = 90 b = 200.362 β = 133.815 c = 144.473 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2010-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97925 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.303 117.1 91.4 0.197 0.251 0.967 4.1 2.4 165206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.303 2.343 96.8 1.201 1.55 0.371 1.3 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.303 104.466 161538 8091 89.342 0.201 0.1996 0.2049 0.226 0.2303 23.181
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.255 -0.519 1.461 -0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.285 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_2_deg 11.463 r_lrange_it 6.995 r_lrange_other 6.995 r_dihedral_angle_1_deg 6.318 r_scangle_it 5.612 r_scangle_other 5.612 r_scbond_it 3.423 r_scbond_other 3.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.285 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_2_deg 11.463 r_lrange_it 6.995 r_lrange_other 6.995 r_dihedral_angle_1_deg 6.318 r_scangle_it 5.612 r_scangle_other 5.612 r_scbond_it 3.423 r_scbond_other 3.423 r_mcangle_other 2.865 r_mcangle_it 2.864 r_mcbond_it 1.817 r_mcbond_other 1.817 r_angle_refined_deg 1.641 r_angle_other_deg 0.823 r_symmetry_nbd_refined 0.5 r_nbd_refined 0.215 r_symmetry_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.183 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_other 0.152 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.072 r_chiral_restr_other 0.055 r_ncsr_local_group_8 0.053 r_ncsr_local_group_16 0.05 r_ncsr_local_group_12 0.049 r_ncsr_local_group_1 0.047 r_ncsr_local_group_3 0.046 r_ncsr_local_group_10 0.046 r_ncsr_local_group_19 0.046 r_ncsr_local_group_18 0.045 r_ncsr_local_group_26 0.045 r_ncsr_local_group_5 0.044 r_ncsr_local_group_7 0.044 r_ncsr_local_group_15 0.044 r_ncsr_local_group_2 0.043 r_ncsr_local_group_9 0.042 r_ncsr_local_group_23 0.042 r_ncsr_local_group_14 0.041 r_ncsr_local_group_13 0.04 r_ncsr_local_group_6 0.039 r_ncsr_local_group_21 0.038 r_ncsr_local_group_25 0.038 r_ncsr_local_group_27 0.038 r_ncsr_local_group_17 0.037 r_ncsr_local_group_24 0.037 r_ncsr_local_group_28 0.036 r_ncsr_local_group_11 0.035 r_ncsr_local_group_22 0.035 r_ncsr_local_group_20 0.034 r_ncsr_local_group_4 0.031 r_bond_refined_d 0.008 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20258 Nucleic Acid Atoms Solvent Atoms 1736 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing